Genotyping including analysis of single nucleotide polymorphisms (SNPs) and gene mutations can provide the basis for “tailor-made medicine”, and the need for genotyping is growing rapidly. With the aim of reducing the side effects of pharmaceuticals, the United States Food and Drug Administration is now trying to make it mandatory for the applicants of new drugs to attach information regarding SNPs and gene mutations relevant to the effect of the drugs. Also in Japan, there is a growing demand for analysis of SNPs and gene mutations.
A device for determining the copy number of a nucleic acid or a mutation(s) in a nucleic acid is used widely for academic and clinical purposes. There have been discovered many biomarkers with which the reactivity to a drug, the prognosis of a disease, etc. can be predicted by examining the copy number of one gene or a mutation(s) in one gene. Examples of such biomarkers include those for Iressa and Herceptin. However, in many cases, high accuracy prediction cannot be achieved with the use of only one biomarker, because the homeostasis in vivo is maintained while being regulated by various networks.
Particularly in recent years, there has been proposed the concept of the “Basin Network”, which is formed by transcription factors and non-coding RNAs (ncRNAs) in relation to each other (Non-Patent Documents 1 to 3). For the maintenance of cell morphology, the limited number of transcription factors and ncRNAs always interact with each other at every level of the central dogma, and in particular, it is considered that the regulation at the transcriptional level contributes greatly to the maintenance of cell morphology. The concentrations of these specific transcription factors and ncRNAs in a nucleus are either constant or oscillating within a given range, and never deviate from the range. Once they deviate, the balance of the network formed between the transcription factors and the ncRNAs in the nucleus changes and shifts to a subsequent form of the network. In this way, the morphology of the cell shifts to a subsequent form such as differentiation, canceration, or senescence.